Explanation for binary files inside source package according to
  http://lists.debian.org/debian-devel/2013/09/msg00332.html

Upstream has provided information about the binary files inside the
source package.  The complete answer is recorded in the ITP bug log at
  http://bugs.debian.org/728285


Files: inst/extdata/CaffeineTxdb.sqlite
Description: stale; removed in future versions.
  sqlite tables derived from querying a public data base ('biomart.org').

Files: inst/extdata/ex1.bam
Description: 
  ex1.sam is the text representation of ex1.bam (using Rsamtools::asBam at the 
  time of file creation); ex1.bam.bai is an index created on ex1.bam (using 
  Rsamtools::indexBam at the time of file creation). ex1.sam is derived from files 
  originally distributed with 'samtools' software under an MIT license, see 
  Rsamtools/LICENSE

Files: inst/extdata/ex1.bcf
  ex1.bcf is a file hand created in antiquity, and used in unit tests and man pages.


Files: inst/extdata/example.gtf.gz.*:
  example.gtf.gz is gz-compressed text file used in unit tests and man pages, hand 
  curated from public data sources, the .tbi variant is an index 
  (Rsamtools::indexTabix)

Files: inst/extdata/example_from_SAM_Spec*:
  This is a file useful to the developer, hand-curated from the SAM spec at
    http://samtools.sourceforge.net/SAMv1.pdf
  although SAM.pdf did not historically include version numbers so the precise 
  origin is unknown.

Files: inst/extdata/olaps.Rda
  The script for creating this file is in the vignette Rsamtools-Overiew.Rnw
 .
 <<readGAlignmentsFromBam, eval=FALSE>>=
 library(parallel)
 options(srapply_fapply="parallel", mc.cores=detectCores())
 olaps <- readGAlignmentsFromBam(bv)
 @

Files: inst/unitTests/cases/ex1.sam.gz
  Except of the first two lines this is a copy of file
    inst/extdata/ex1.sam

Files: inst/unitTests/cases/ex1_*.bam*
  Files are derived from file
    inst/extdata/ex1.sam
  and just used for verification of the correctness of
  Rsamtools.

Files: inst/unitTests/cases/plp_refskip.bam*
  This is a hand-crafted file used in a unit test


Source code duplication
=======================

The following files are copies of source code that is just contained in
other Debian packages.  We are discussing this issue with upstream to
enable making use of dynamic linking for future versions of this package.

Files: src/samtools/*
 Source is part of samtools (0.1.19-1)
 For more details what was tried see
   debian/patches/use-debian-packaged-libs.patch

Files: src/tabix/*
 Source is part of tabix (0.2.6-1)


 -- Andreas Tille <tille@debian.org>  Fri, 25 Oct 2013 08:53:18 +0200
